Here are the answers to the questions:

1. What tool was used for pathway enrichment analysis?
The tool used for pathway enrichment analysis is not explicitly described, but it appears that an R package named "q-value" was used to calculate the Q-values, which represent the false discovery rate (FDR).

2. Was a tool version number provided?
Not described.

3. What gene set library was queried (eg: GO, KEGG, Reactome or other)?
The article mentions that rice proteins were mapped to multiple public databases, including Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG), suggesting that these libraries were queried.

4. Was a background gene list defined for pathway enrichment analysis?
Yes, the article states that "using all the proteins as background" was used to calculate the p-value and Q-value.

5. What statistical test was used for enrichment analysis?
Fisher's exact test was used to calculate the p-values.

6. Was false discovery rate correction used to control the number of false positives in the pathway enrichment analysis?
Yes, the article states that the Q-values were calculated by an R package named "q-value" and that the threshold of significance was defined as FDR < 0.05.